Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • Navigation/Query Panel:
    Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
    description Network Comparison Type Rank Gene Hugo Interaction Map Value Type Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 382 to 431 of 515 in total
    Network Comparison Type  : Subtracted
    Value Type  : Ranked
    Filtered  : 1
    red  : 0
    green  : 0
    network_comparison  : 0
    description
    		Rank
    		Hugo
    		Interaction Map
    sex comb on midleg-like 2; sex comb on midleg like 2. [refseq;acc:nm_006089] 3120 SCML2 High confidence
    sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503] 2794 SH2B1
    sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3] 2867 no value
    signal recognition particle 14 kda protein (srp14) (18 kda alu rna binding protein). [swissprot;acc:p37108] 5032 SRP14 Low confidence
    similar to cg5057 gene product. [sptrembl;acc:q9btt4] 2984 MED10 High confidence
    similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] 3032 LYZL1
    similar to mob-lak. [refseq;acc:nm_145279] 2937 MOBKL2C
    skd1 protein (vacuolar sorting protein 4b). [swissprot;acc:o75351] 3037 VPS4B
    skeletal muscle and kidney enriched inositol phosphatase isoform 1; 43-kda form skeletal muscle and kidney enriched inositol phosphatase. [refseq;acc:nm_016532] 2994 no value
    small edrk-rich factor 2. [refseq;acc:nm_005770] 2947 SERF2
    small nuclear ribonucleoprotein associated protein n (snrnp-n) (sm protein n) (sm-n) (smn) (sm-d) (tissue-specific splicing protein). [swissprot;acc:p14648] 3004 SNRPN
    small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678] 3012 SNRPB
    snrna activating protein complex 50 kda subunit (snapc 50 kda subunit) (proximal sequence element-binding transcription factor beta subunit) (pse-binding factor beta subunit) (ptf beta subunit). [swissprot;acc:q92966] 2849 SNAPC3
    solute carrier family 21 member 15 (organic anion transporter polypeptide-related protein 4) (oatp-rp4) (oatprp4). [swissprot;acc:q9h2y9] 2965 SLCO5A1
    5034 Low confidence
    solute carrier family 36 member 1; proton / amino acid symporter; lysosomal amino acid transporter 1. [refseq;acc:nm_078483] 3026 SLC36A1 High confidence
    sorting nexin 16. [swissprot;acc:p57768] 3108 SNX16
    sparc precursor (secreted protein acidic and rich in cysteine) (osteonectin) (on) (basement membrane protein bm-40). [swissprot;acc:p09486] 3062 SPARC
    sparc-like protein 1 precursor (high endothelial venule protein) (hevin) (mast 9). [swissprot;acc:q14515] 2899 SPARCL1
    spartin; trans-activated by hepatitis c virus core protein 1. [refseq;acc:nm_015087] 2987 SPG20
    speckle-type poz protein. [swissprot;acc:o43791] 3031 SPOP
    spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813] 3038 no value
    sperm tail protein shippo1; h-shippo 1. [refseq;acc:nm_053280] 2797 ODF3
    spermine synthase (ec 2.5.1.22) (spermidine aminopropyltransferase) (spmsy). [swissprot;acc:p52788] 3118 SMS
    spinster-like protein. [sptrembl;acc:q9h2v7] 5023 SPNS1 Low confidence
    spir-2 protein (fragment). [sptrembl;acc:q8wwl2] 2879 no value High confidence
    spry domain-containing socs box protein ssb-1. [refseq;acc:nm_025106] 2814 SPSB1
    spry domain-containing socs box protein ssb-4. [refseq;acc:nm_080862] 2806 SPSB4
    ss18-like protein 1 (syt homolog-1). [swissprot;acc:o75177] 2766 SS18L1
    ssxt protein (synovial sarcoma, translocated to x chromosome) (syt protein). [swissprot;acc:q15532] 2942 SS18
    ste20-like kinase; ste2-like kinase. [refseq;acc:nm_016281] 2980 TAOK3
    steroidogenic factor 1 (stf-1) (sf-1) (steroid hormone receptor ad4bp) (fushi tarazu factor homolog 1). [swissprot;acc:q13285] 2972 NR5A1
    suppressor of actin 1. [refseq;acc:nm_014016] 2826 no value
    syndecan-3 (synd3). [swissprot;acc:o75056] 2862 SDC3
    syntaxin 5. [swissprot;acc:q13190] 2866 STX5
    t-box transcription factor tbx1 (t-box protein 1) (testis-specific t-box protein). [swissprot;acc:o43435] 2771 TBX1
    t-cell acute lymphocytic leukemia-1 protein (tal-1 protein) (stem cell protein) (t-cell leukemia/lymphoma-5 protein). [swissprot;acc:p17542] 2865 TAL1
    t-cell acute lymphocytic leukemia-2 protein (tal-2 protein). [swissprot;acc:q16559] 2760 TAL2
    t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227] 2917 CCT6A
    t-complex protein 1, zeta-2 subunit (tcp-1-zeta-2) (cct-zeta-2) (tcp- 1-zeta-like) (cct-zeta-like) (testis-specific tcp20) (testis-specific protein tsa303). [swissprot;acc:q92526] 2995 CCT6B
    taube nuss. [refseq;acc:nm_138572] 2967 TAF8
    tektin 2 (tektin-t) (testicular tektin b1-like protein). [swissprot;acc:q9uif3] 3156 TEKT2
    testis intracellular mediator protein. [refseq;acc:nm_057161] 3019 KLHDC3
    testis specific leucine rich repeat protein. [refseq;acc:nm_012472] 3003 LRRC6
    5038 Low confidence
    testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562] 3021 CRISP2 High confidence
    tetratricopeptide repeat protein 1 (tpr repeat protein 1). [swissprot;acc:q99614] 3060 TTC1
    thousand and one amino acid protein kinase. [refseq;acc:nm_004783] 2906 TAOK2
    thymidine kinase 2, mitochondrial precursor (ec 2.7.1.21) (mt-tk). [swissprot;acc:o00142] 2837 TK2
    5024 Low confidence

    Legend:
    - Rank is the rank after comparing the two networks
    - Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
    - Hugo is the HGNC identifier if it exists
    - Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
    - Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
    - Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
    - Filtered specifies whether we only included the high confidence microarry measurements or not.
    - http://analysis.yellowcouch.org/